US20050255488A1 - NTRK1 genetic markers associated with age of onset of Alzheimer's Disease - Google Patents

NTRK1 genetic markers associated with age of onset of Alzheimer's Disease Download PDF

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US20050255488A1
US20050255488A1 US10/962,756 US96275604A US2005255488A1 US 20050255488 A1 US20050255488 A1 US 20050255488A1 US 96275604 A US96275604 A US 96275604A US 2005255488 A1 US2005255488 A1 US 2005255488A1
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haplotype
age
individual
haplotypes
onset
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Jeroen Aerssens
Maria Athanasiou
Carlos Brain
Nadine Cohen
Bradley Dain
R. Denton
Richard Judson
Vural Ozdemir
Carol Reed
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Janssen Pharmaceutica NV
PGxHealth LLC
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Genaissance Pharmaceuticals Inc
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • G01N33/6896—Neurological disorders, e.g. Alzheimer's disease
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • This invention relates to the fields of genomics and pharmacogenomics. More specifically, this invention relates to variants of the gene encoding neurotrophic tyrosine kinase, receptor, type 1 (NTRK1) and their association with age of onset of Alzheimer's Disease.
  • NRRK1 neurotrophic tyrosine kinase, receptor, type 1
  • AD Alzheimer's Disease
  • Sporadic AD a late-onset form of the disease, is the most common form of AD, and generally only occurs in people who are at least 65.
  • Familial AD an early-onset form of the disease, and accounting for only about 5% of all AD cases, generally affects people between the ages of 30 and 65.
  • the average worldwide risk of developing any type of AD is about 5% by age 65, 10 to 15% by age 75, and 20 to 40% by age 85.
  • AD sporadic AD
  • genetic factors are believed to be involved, as evidenced by an increased risk of AD in individuals who have a family history of AD (Devi et al., Arch. Neurol. 57:28-9 (2000)) or who have one or more of several specific polymorphisms that have been correlated with increased risk for AD.
  • Known genetic polymorphisms that are risk factors for developing AD include the apolipoprotein E (APOE) ⁇ 4 allele (U.S. Pat. No. 5,508,167); the ⁇ 1-antichymotrypsin (ACT) A allele (U.S. Pat. No. 5,773,220), and the interleukin-1 (IL-1) A 2,2 and IL-1B 2,2 genotypes (U.S. Pat. No. 6,225,069 B1).
  • APOE apolipoprotein E
  • ACT ⁇ 1-antichymotrypsin
  • IL-1 interleukin-1
  • IL-1 interleukin-1
  • MCI mild or minimal cognitive impairment
  • AD cognitive and behavioral deficits observed in AD are believed to be primarily related to the degeneration of basal forebrain cholinergic neurons (BFCNs) (Capsoni et al., Proc. Natl. Acad. Sci. USA 99:12432-12437 (2002).
  • nerve growth factor influences the cholinergic phenotype of BFCNs by promoting their survival and differentiation during development and adulthood, it has been suggested that decreased NGF function could contribute to the onset of AD (Capsoni et al., supra).
  • NGF function A connection between NGF function and AD is supported by a recent report that administration of NGF largely reversed the early phases of neurodegeneration induced by expression of anti-NGF antibodies in a transgenic mouse model of AD (Capsoni et al., supra). Interestingly, the cholinergic deficit in this mouse model of AD was also largely rescued by early administration of galantamine, which has both AChE-inhibiting activity and nicotinic agonist activity, but not by early administration of the powerful AChE inhibitors tacrine and physostigmine (Capsoni et al., supra).
  • NTRK1 is the high affinity receptor for NGF and is also referred to as tyrosine kinase receptor (TRK) and tyrosine kinase receptor A (TRKA).
  • TRK tyrosine kinase receptor
  • TRKA tyrosine kinase receptor A
  • NTRK1 mRNA and NTRK1 protein have been observed in cholinergic cells in late stage AD (Boissiere et al., Exp. Neurol. 145:245-52 (1997)).
  • a recent study found that patients diagnosed with MCI had reduced NTRK1 mRNA levels of a similar magnitude to the reduced levels of NTRK1 mRNA found in AD patients, relative to age-matched controls, and that these reduced levels in both MCI and AD patients were significantly correlated with function on a variety of episodic memory tests (Chu et al., J. Comp. Neurol. 437:296-307 (2001)).
  • NTRK1 phosphorylates certain tyrosine residues in the cytoplasmic tail of beta-amyloid precursor protein (APP), a widely expressed transmembrane protein of unknown function that is involved in the pathogenesis of AD (Tarr et al., J. Biol. Chem. 277:16798-804 (2002)).
  • APP beta-amyloid precursor protein
  • the gene for NTRK1 is located on chromosome 1q23-q31 and spans at least 23 kb and is split into 17 exons, of which exon 9 is alternatively spliced (Indo et al., Jpn. J. Hum. Genet. 42(2):343-51 (1997); Greco et al., Oncogene 13:2463-6 (1996)).
  • a reference sequence for the NTRK1 gene is shown in FIG. 1 (from GenBank Accession No. AL158169.17).
  • CIPA congenital insensitivity to pain with anhidrosis
  • a number of other NTRK1 gene polymorphisms have also been identified. However, there are no reports of any of these NTRK1 gene mutations or polymorphisms being associated with reduced cognitive function, MCI or AD.
  • NTRK1 Because of the possible involvement of NTRK1 in the cognitive deficits observed in MCI and early stages of AD, and the need for additional ways to identify people with these conditions, it would be useful to assess the degree of variation in the NTRK1 gene in patients with AD and to determine if any variants of this gene are associated with the age of AD onset.
  • the inventors herein have discovered a set of haplotypes in the NTRK1 gene that are associated with the age of onset of AD.
  • the inventors have also discovered that the copy number of each of these NTRK1 haplotypes affects the age of onset of AD. Testing for the presence or absence, and copy number, of these haplotypes is useful for predicting the age at which individuals who are at increased risk for AD are likely to develop AD and to help confirm a diagnosis of MCI or AD. Such knowledge will help individuals with MCI or AD, as well as their physicians and families, make therapy and lifestyle decisions.
  • NTRK1 haplotypes are shown in Table 1 below.
  • haplotypes may readily be identified based on linkage disequilibrium between any of the above NTRK1 haplotypes and another haplotype located in the NTRK1 gene or another gene, or between an allele at one or more of the PSs in the above haplotypes and an allele at another PS located in the NTRK1 gene or another gene.
  • haplotypes include haplotypes that are in linkage disequilibrium with any of haplotypes (1)-(112) in Table 1, hereinafter referred to as “linked haplotypes,” as well as “substitute haplotypes” for any of haplotypes (1)-(112) in which one or more of the polymorphic sites (PSs) in the original haplotype is substituted with another PS, wherein the allele at the substituted PS is in linkage disequilibrium with the allele at the substituting PS.
  • linked haplotypes any of haplotypes (1)-(112) in Table 1, hereinafter referred to as “linked haplotypes,” as well as “substitute haplotypes” for any of haplotypes (1)-(112) in which one or more of the polymorphic sites (PSs) in the original haplotype is substituted with another PS, wherein the allele at the substituted PS is in linkage disequilibrium with the allele at the substituting PS.
  • PSs polymorphic
  • the invention provides methods and kits for determining whether an individual has an age of onset marker I or an age of onset marker II.
  • a method is provided for determining whether an individual has an age of onset marker I or an age of onset marker II comprising determining whether the individual has zero copies or at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1.
  • a method for assigning an individual to a first or second age of onset marker group comprising determining whether the individual has zero copies or at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1; and assigning the individual to an age of onset marker group based on the copy number of that haplotype.
  • the individual is assigned to the first age of onset marker group if the individual has at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1, and is assigned to the second age of onset marker group if the individual has zero copies of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1.
  • kits for determining whether an individual has an age of onset marker I or an age of onset marker II comprises a set of oligonucleotides designed for identifying at least one of the alleles present at each PS in a set of one or more PSs.
  • the set of one or more PSs comprises the set of one or more PSs for any of the haplotypes in Table 1, the set of one or more PSs for a linked haplotype for any of the haplotypes in Table 1, or the set of one or more PSs for a substitute haplotype for any of the haplotypes in Table 1.
  • the kit comprises a manual with instructions for performing one or more reactions on a human nucleic acid sample to identify the allele(s) present in the individual at each PS in the set and determining if the individual has an age of onset marker I or an age of onset marker II based on the identified allele(s).
  • the invention further provides a method for delaying the onset of AD in an individual at risk for developing AD.
  • the method comprises determining whether the individual has an age of onset marker I or an age of onset marker II and making a treatment decision for the individual based on the results of the determining step. If the individual is determined to have an age of onset marker I, then the treatment decision is to prescribe to the individual a compound effective in delaying the onset of AD, wherein the compound is prescribed to the individual at an age that is below that of the lower confidence interval of the least square mean of age of onset for the age of onset marker I.
  • the treatment decision is to prescribe to the individual a compound effective in delaying the onset of AD, wherein the compound is prescribed to the individual at an age that is below that of the lower confidence interval of the least square mean of age of onset for the age of onset marker II.
  • the lower confidence interval of the least square mean of age of onset for an age of onset marker I ranges from 69.8 to 70.5
  • the lower confidence interval of the least square mean of age of onset for an age of onset marker II ranges from 65.3 to 65.9.
  • the invention provides a method for predicting an individual's age of onset of AD.
  • the method comprises determining whether the individual has an age of onset marker I or an age of onset marker II and making an prediction based on the results of the determining step. According to Table 8 below, if the individual is determined to have an age of onset marker I, then the prediction is that the individual's age of onset of AD will be between 71.6 and 73.3, and if the individual is determined to have an age of onset marker II, then the prediction is that the individual's age of onset of AD will be between 65.3 and 70.5.
  • the invention provides (i) a method for seeking regulatory approval for marketing a pharmaceutical formulation comprising, as at least one active ingredient, a compound effective in delaying the onset of AD, to a population at risk for developing AD, wherein the population is partially or wholly defined by having an age of onset marker I or an age of onset marker II, (ii) an article of manufacture comprising the pharmaceutical formulation, (iii) a method for manufacturing a drug product comprising the pharmaceutical formulation, and (iv) a method for marketing the drug product.
  • the method for seeking regulatory approval comprises conducting at least one clinical trial which comprises administering the pharmaceutical formulation to first and second groups of individuals at risk for developing AD, and administering a placebo to third and fourth groups of individuals at risk for developing AD, wherein each individual in the first and third groups has an age of onset marker I, and each individual in the second and fourth groups has an age of onset marker II, demonstrating that the first group exhibits a later onset of AD than the third group, and demonstrating that the second group exhibits a later onset of AD than the fourth group, and filing with a regulatory agency an application for marketing approval of the pharmaceutical formulation with a label stating that the pharmaceutical formulation is indicated for delaying the onset of AD in a population at risk for developing AD.
  • the regulatory agency is the United States Food and Drug Administration (FDA) or the European Agency for the Evaluation of Medicinal Products (EMEA), or a future equivalent of these agencies.
  • the article of manufacture comprises the pharmaceutical formulation and at least one indicium identifying a population for whom the pharmaceutical formulation is indicated, wherein the identified population is at risk for developing AD and is partially or wholly defined by having an age of onset marker I or an age of onset marker II, wherein a trial population of individuals having an age of onset marker I exhibit a later age of onset of AD than a trial population having an age of onset marker II.
  • the article of manufacture comprises packaging material and the pharmaceutical formulation contained within the packaging material, wherein the packaging material comprises a label approved by a regulatory agency for the pharmaceutical formulation, wherein the label states that the pharmaceutical formulation is indicated for a population at risk for developing AD that is partially or wholly defined by having an age of onset marker I or an age of onset marker II, and preferably further stating that a trial population of individuals having an age of onset marker I exhibit a later age of onset of AD than a trial population of individuals having an age of onset marker II.
  • the pharmaceutical formulation comprises, as at least one active ingredient, a compound effective in delaying the onset of AD.
  • the method for manufacturing the drug product comprises combining in a package a pharmaceutical formulation comprising, as at least one active ingredient, a compound effective in delaying the onset of AD, and a label which states that the drug product is indicated for a population at risk for developing AD, wherein the population is partially or wholly defined by having an age of onset marker I or an age of onset marker II, wherein those members of the population having an age of onset marker I exhibit a later age of onset of AD than those members of the population having an age of onset marker II.
  • the method for marketing the drug product comprises promoting to a target audience the use of the drug product for treating individuals who belong to the defined population
  • FIG. 1A -J illustrates a reference sequence for the NTRK1 gene (contiguous lines; SEQ ID NO:1), with the start and stop positions of each region of coding sequence indicated with a bracket ([ or ]) and the numerical position below the sequence and the polymorphic site(s) and polymorphism(s) identified in the patient cohort indicated by the variant nucleotide positioned below the polymorphic site in the sequence.
  • Allele A particular form of a genetic locus, distinguished from other forms by its particular nucleotide sequence, or one of the alternative polymorphisms found at a polymorphic site.
  • Gene A segment of DNA that contains the coding sequence for a protein, wherein the segment may include promoters, exons, introns, and other untranslated regions that control expression.
  • Genotype An unphased 5′ to 3′ sequence of nucleotide pair(s) found at a set of one or more polymorphic sites in a locus on a pair of homologous chromosomes in an individual.
  • genotype includes a full-genotype and/or a sub-genotype as described below.
  • Genotyping A process for determining a genotype of an individual.
  • Haplotype A 5′ to 3′ sequence of nucleotides found at a set of one or more polymorphic sites in a locus on a single chromosome from a single individual.
  • Haplotype pair The two haplotypes found for a locus in a single individual.
  • Haplotyping A process for determining one or more haplotypes in an individual and includes use of family pedigrees, molecular techniques and/or statistical inference.
  • Haplotype data Information concerning one or more of the following for a specific gene: a listing of the haplotype pairs in an individual or in each individual in a population; a listing of the different haplotypes in a population; frequency of each haplotype in that or other populations, and any known associations between one or more haplotypes and a trait.
  • Isolated As applied to a biological molecule such as RNA, DNA, oligonucleotide, or protein, isolated means the molecule is substantially free of other biological molecules such as nucleic acids, proteins, lipids, carbohydrates, or other material such as cellular debris and growth media. Generally, the term “isolated” is not intended to refer to a complete absence of such material or to absence of water, buffers, or salts, unless they are present in amounts that substantially interfere with the methods of the present invention.
  • Locus A location on a chromosome or DNA molecule corresponding to a gene or a physical or phenotypic feature, where physical features include polymorphic sites.
  • Nucleotide pair The nucleotides found at a polymorphic site on the two copies of a chromosome from an individual.
  • phased As applied to a sequence of nucleotide pairs for two or more polymorphic sites in a locus, phased means the combination of nucleotides present at those polymorphic sites on a single copy of the locus is known.
  • PS Polymorphic site
  • Polymorphism The sequence variation observed in an individual at a polymorphic site. Polymorphisms include nucleotide substitutions, insertions, deletions and microsatellites and may, but need not, result in detectable differences in gene expression or protein function.
  • Polynucleotide A nucleic acid molecule comprised of single-stranded RNA or DNA or comprised of complementary, double-stranded DNA.
  • Population Group A group of individuals sharing a common ethnogeographic origin.
  • Reference Population A group of subjects or individuals who are predicted to be representative of the genetic variation found in the general population. Typically, the reference population represents the genetic variation in the population at a certainty level of at least 85%, preferably at least 90%, more preferably at least 95% and even more preferably at least 99%.
  • Subject A human individual whose genotypes or haplotypes or age of onset to treatment or disease state are to be determined.
  • Treatment A stimulus administered internally or externally to a subject.
  • Unphased As applied to a sequence of nucleotide pairs for two or more polymorphic sites in a locus, unphased means the combination of nucleotides present at those polymorphic sites on a single copy of the locus is not known.
  • Each age of onset marker of the invention is a combination of a particular haplotype and the copy number for that haplotype.
  • the haplotype is one of the haplotypes shown in Table 1.
  • the PS or PSs in these haplotypes are referred to herein as PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, and PS12 and are located in the NTRK1 gene at positions corresponding to those identified in FIG. 1 /SEQ ID NO:1 (see Table 2 for summary of PS1, PS2, PS3, PS4, PS5, PS6, PS7, PS8, PS9, PS10, PS11, and PS12 and locations).
  • nucleic acid molecules containing a particular gene may be complementary double stranded molecules and thus reference to a particular site or haplotype on the sense strand refers as well to the corresponding site or haplotype on the complementary antisense strand. Further, reference may be made to detecting a genetic marker or haplotype for one strand and it will be understood by the skilled artisan that this includes detection of the complementary haplotype on the other strand.
  • the age of onset markers of the invention are based on the discovery by the inventors of associations between certain haplotypes in the NTRK1 gene and the age of onset of AD in a cohort of individuals diagnosed with AD.
  • haplotype comprising cytosine at PS5, guanine at PS10, and thymine at PS11 (haplotype (7) in Table 1) affected the age of onset of AD of the patients participating in the study.
  • the group of patients having at least one copy of this haplotype experienced a later age of onset of AD than the patient group having zero copies of the haplotype.
  • the linked haplotype is present in the NTRK1 gene or in a genomic region of about 100 kilobases spanning the NTRK1 gene.
  • the linkage disequilibrium between the haplotypes in Table 1 and such linked haplotypes can also be measured using ⁇ 2 .
  • the linkage disequilibrium between an allele at a polymorphic site in any of the haplotypes in Table 1 and an allele at a “substituting” polymorphic site, or between any of the haplotypes in Table 1 and a linked haplotype has a ⁇ 2 value, as measured in a suitable reference population, of at least 0.75, more preferably at least 0.80, even more preferably at least 0.85 or at least 0.90, yet more preferably at least 0.95, and most preferably 1.0.
  • a suitable reference population for this ⁇ 2 measurement is selected from a population with the distribution of its members reflecting the general population, a population with AD or AD risk factors, and the like.
  • LD patterns in genomic regions are readily determined empirically in appropriately chosen samples using various techniques known in the art for determining whether any two alleles (either those occurring at two different PSs or two haplotypes for two different multi-site loci) are in linkage disequilibrium (G ENETIC D ATA A NALYSIS II, Weir, Sinauer Associates, Inc. Publishers, Sunderland, Mass., 1996). The skilled artisan may readily select which method of determining LD will be best suited for a particular sample size and genomic region.
  • the age of onset markers of the invention are associated with differences in the age of onset of AD.
  • the invention provides a method and kit for determining whether an individual has an age of onset marker I or an age of onset marker II.
  • An age of onset marker I is at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1.
  • An age of onset marker II is zero copies of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1.
  • the invention provides a method for determining whether an individual has an age of onset marker I or an age of onset marker II.
  • the method comprises determining whether the individual has zero copies or at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1.
  • the method comprises determining whether the individual has zero copies or at least one copy of any of (a) haplotype (1) in Table 1, (a) a linked haplotype for haplotype (1) in Table 1, and (b) a substitute haplotype for haplotype (1) in Table 1.
  • the individual is Caucasian and is at risk for developing a cognitive disorder, such as mild to moderate dementia of the Alzheimer's type, dementia associated with Parkinson's Disease, MCI, a vascular dementia, and Lewy body dementia.
  • a cognitive disorder such as mild to moderate dementia of the Alzheimer's type, dementia associated with Parkinson's Disease, MCI, a vascular dementia, and Lewy body dementia.
  • the invention provides a method for assigning an individual to a first or second age of onset marker group.
  • the method comprises determining whether the individual has zero copies or at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1, and assigning the individual to the first age of onset marker group if the individual has at least one copy of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes (1)-(112) in Table 1, and (c) a substitute haplotype for any of haplotypes (1)-(112) in Table 1, and assigning the individual to the second age of onset marker group if the individual has zero copies of any of (a) haplotypes (1)-(112) in Table 1, (b) a linked haplotype for any of haplotypes
  • the individual is Caucasian and is at risk for developing a cognitive disorder, such as mild to moderate dementia of the Alzheimer's type, dementia associated with Parkinson's Disease, MCI, a vascular dementia, and Lewy body dementia.
  • a cognitive disorder such as mild to moderate dementia of the Alzheimer's type, dementia associated with Parkinson's Disease, MCI, a vascular dementia, and Lewy body dementia.
  • the presence in an individual of an age of onset marker I or an age of onset marker II may be determined by a variety of indirect or direct methods well known in the art for determining haplotypes or haplotype pairs for a set of one or more PSs in one or both copies of the individual's genome, including those discussed below.
  • the genotype for a PS in an individual may be determined by methods known in the art or as described below.
  • One indirect method for determining whether zero copies, one copy, or two copies of a haplotype is present in an individual is by prediction based on the individual's genotype determined at one or more of the PSs comprising the haplotype and using the determined genotype at each site to determine the haplotypes present in the individual.
  • the presence of zero copies, one copy, or two copies of a haplotype of interest can be determined by visual inspection of the alleles at the PS that comprise the haplotype.
  • the haplotype pair is assigned by comparing the individual's genotype with the genotypes at the same set of PS corresponding to the haplotype pairs known to exist in the general population or in a specific population group or to the haplotype pairs that are theoretically possible based on the alternative alleles possible at each PS, and determining which haplotype pair is most likely to exist in the individual.
  • this haplotype pair prediction method comprises identifying a genotype for the individual at the set of PSs comprising the selected haplotype, accessing data containing haplotype pairs identified in a reference population for a set of PSs comprising the PSs of the selected haplotype, and assigning to the individual a haplotype pair that is consistent with the individual's genotype.
  • the haplotype pair can be assigned by comparing the individual's genotype with the genotypes corresponding to the haplotype pairs known to exist in the general population or in a specific population group, and determining which haplotype pair is consistent with the genotype of the individual. In some embodiments, the comparing step may be performed by visual inspection. When the genotype of the individual is consistent with more than one haplotype pair, frequency data may be used to determine which of these haplotype pairs is most likely to be present in the individual.
  • haplotype pair frequency data used in this determination is preferably for a reference population comprising the same ethnogeographic group as the individual. This determination may also be performed in some embodiments by visual inspection. In other embodiments, the comparison may be made by a computer-implemented algorithm with the genotype of the individual and the reference haplotype data stored in computer-readable formats.
  • one computer-implemented algorithm to perform this comparison entails enumerating all possible haplotype pairs which are consistent with the genotype, accessing data containing haplotype pairs frequency data determined in a reference population to determine a probability that the individual has a possible haplotype pair, and analyzing the determined probabilities to assign a haplotype pair to the individual.
  • the reference population is composed of randomly selected individuals representing the major ethnogeographic groups of the world.
  • a preferred reference population allows the detection of any haplotype whose frequency is at least 10% with about 99% certainty.
  • a particularly preferred reference population includes a 3-generation Caucasian family to serve as a control for checking quality of haplotyping procedures.
  • a statistically significant difference between the observed and expected haplotype frequencies could be due to one or more factors including significant inbreeding in the population group, strong selective pressure on the gene, sampling bias, and/or errors in the genotyping process. If large deviations from Hardy-Weinberg equilibrium are observed in an ethnogeographic group, the number of individuals in that group can be increased to see if the deviation is due to a sampling bias. If a larger sample size does not reduce the difference between observed and expected haplotype pair frequencies, then one may wish to consider haplotyping the individual using a direct haplotyping method such as, for example, CLASPER SystemTM technology ((U.S. Pat. No. 5,866,404), single molecule dilution, or allele-specific long-range PCR (Michalotos-Beloin et al., Nucleic Acids Res. 24:4841-3 (1996)).
  • CLASPER SystemTM technology (U.S. Pat. No. 5,866,404)
  • single molecule dilution single molecule
  • the assigning step involves performing the following analysis. First, each of the possible haplotype pairs is compared to the haplotype pairs in the reference population. Generally, only one of the haplotype pairs in the reference population matches a possible haplotype pair and that pair is assigned to the individual. Occasionally, only one haplotype represented in the reference haplotype pairs is consistent with a possible haplotype pair for an individual, and in such cases the individual is assigned a haplotype pair containing this known haplotype and a new haplotype derived by subtracting the known haplotype from the possible haplotype pair.
  • the haplotype pair in an individual may be predicted from the individual's genotype for that gene using reported methods (e.g., Clark et al., Mol. Biol. Evol. 7:1121-22 (1990) or WO 01/80156) or through a commercial haplotyping service such as offered by Genaissance Pharmaceuticals, Inc. (New Haven, Conn.).
  • a direct molecular haplotyping method such as, for example, CLASPER SystemTM technology (U.S. Pat. No. 5,866,404), SMD, or allele-specific long-range PCR (Michalotos-Beloin et al., supra).
  • haplotype (7) Determination of the number of haplotypes present in the individual from the genotypes is illustrated here for haplotype (7) in Table 1.
  • Table 3 shows the 27 (3 n , where each of n bi-allelic polymorphic sites may have one of 3 different genotypes present) genotypes that may be detected at PS5, PS10 and PS11, using both chromosomal copies from an individual. 24 of the 27 possible genotypes for the two sites allow unambiguous determination of the number of copies of the haplotype (7) in Table 1 present in the individual and therefore would allow unambiguous determination of whether the individual has an age of onset marker I or an age of onset marker II.
  • an individual with the C/C G/T C/T genotype could possess one of the following haplotype pairs: CGC/CTT, CTT/CGC, CTC/CGT, or CGT/CTG, and thus could have either one copy of haplotype (7) in Table 1 (CTC/CGT, CGT/CTG) corresponding to an age of onset marker I, or zero copies (CGC/CTT, CTT/CGC) of haplotype (7) in Table 1 corresponding to an age of onset marker II.
  • CTC/CGT, CGT/CTG CTC/CGT
  • CGT/CTG zero copies
  • CGC/CTT, CTT/CGC CTT/CGC
  • frequency information may be used to determine the most probable haplotype pair and therefore the most likely number of copies of the haplotype in the individual. If a particular haplotype pair consistent with the genotype of the individual is more frequent in the reference population than other pairs consistent with the genotype, then that haplotype pair with the highest frequency is the most likely to be present in the individual.
  • the copy number of the haplotype of interest in this haplotype pair can then be determined by visual inspection of the alleles at the PS that comprise the age of onset marker for each haplotype in the pair.
  • genotyping of one or more additional sites in NTRK1 may be performed to eliminate the ambiguity in deconvoluting the haplotype pairs underlying the genotype at the particular PSs.
  • the skilled artisan would recognize that alleles at these one or more additional sites would need to have sufficient linkage with the alleles in at least one of the possible haplotypes in the pair to permit unambiguous assignment of the haplotype pair.
  • this illustration has been directed to the particular instance of determining the number of copies of haplotype (7) in Table 1 present in an individual, the process would be analogous for the other haplotypes shown in Table 1, or for the linked haplotypes or substitute haplotypes for any of the haplotypes in Table 1.
  • the individual's genotype for the desired set of PS may be determined using a variety of methods well-known in the art. Such methods typically include isolating from the individual a genomic DNA sample comprising both copies of the gene or locus of interest, amplifying from the sample one or more target regions containing the polymorphic sites to be genotyped, and detecting the nucleotide pair present at each PS of interest in the amplified target region(s). It is not necessary to use the same procedure to determine the genotype for each PS of interest.
  • the identity of the allele(s) present at any of the novel PSs described herein may be indirectly determined by haplotyping or genotyping another PS having an allele that is in linkage disequilibrium with an allele of the PS that is of interest.
  • PSs having an allele in linkage disequilibrium with an allele of the presently disclosed PSs may be located in regions of the gene or in other genomic regions not examined herein.
  • Detection of the allele(s) present at a PS, wherein the allele is in linkage disequilibrium with an allele of the novel PSs described herein may be performed by, but is not limited to, any of the above-mentioned methods for detecting the identity of the allele at a PS.
  • the presence in an individual of a haplotype or haplotype pair for a set of PSs comprising an age of onset marker may be determined by directly haplotyping at least one of the copies of the individual's genomic region of interest, or suitable fragment thereof, using methods known in the art.
  • Such direct haplotyping methods typically involve treating a genomic nucleic acid sample isolated from the individual in a manner that produces a hemizygous DNA sample that only has one of the two “copies” of the individual's genomic region which, as readily understood by the skilled artisan, may be the same allele or different alleles, amplifying from the sample one or more target regions containing the PSs to be genotyped, and detecting the nucleotide present at each PS of interest in the amplified target region(s).
  • the nucleic acid sample may be obtained using a variety of methods known in the art for preparing hemizygous DNA samples, which include: targeted in vivo cloning (TIVC) in yeast as described in WO 98/01573, U.S. Pat.
  • any individual clone will typically only provide haplotype information on one of the two genomic copies present in an individual. If haplotype information is desired for the individual's other copy, additional clones will usually need to be examined. Typically, at least five clones should be examined to have more than a 90% probability of haplotyping both copies of the genomic locus in an individual. In some cases, however, once the haplotype for one genomic allele is directly determined, the haplotype for the other allele may be inferred if the individual has a known genotype for the PSs of interest or if the haplotype frequency or haplotype pair frequency for the individual's population group is known.
  • direct haplotyping of both copies of the gene is preferably performed with each copy of the gene being placed in separate containers, it is also envisioned that direct haplotyping could be performed in the same container if the two copies are labeled with different tags, or are otherwise separately distinguishable or identifiable. For example, if first and second copies of the gene are labeled with different first and second fluorescent dyes, respectively, and an allele-specific oligonucleotide labeled with yet a third different fluorescent dye is used to assay the PS(s), then detecting a combination of the first and third dyes would identify the polymorphism in the first gene copy while detecting a combination of the second and third dyes would identify the polymorphism in the second gene copy.
  • the nucleic acid sample used in the above indirect and direct haplotyping methods is typically isolated from a biological sample taken from the individual, such as a blood sample or tissue sample.
  • tissue samples include whole blood, saliva, tears, urine, skin and hair.
  • the target region(s) containing the PS of interest may be amplified using any oligonucleotide-directed amplification method, including but not limited to polymerase chain reaction (PCR) (U.S. Pat. No. 4,965,188), ligase chain reaction (LCR) (Barany et al., Proc. Natl. Acad. Sci. USA 88:189-93 (1991); WO 90/01069), and oligonucleotide ligation assay (OLA) (Landegren et al., Science 241:1077-80 (1988)).
  • PCR polymerase chain reaction
  • LCR ligase chain reaction
  • OLA oligonucleotide ligation assay
  • Other known nucleic acid amplification procedures may be used to amplify the target region(s) including transcription-based amplification systems (U.S. Pat. No.
  • the identity of a nucleotide (or nucleotide pair) at a PS(s) in the amplified target region may be determined by sequencing the amplified region(s) using conventional methods. If both copies of the gene are represented in the amplified target, it will be readily appreciated by the skilled artisan that only one nucleotide will be detected at a PS in individuals who are homozygous at that site, while two different nucleotides will be detected if the individual is heterozygous for that site.
  • the polymorphism may be identified directly, known as positive-type identification, or by inference, referred to as negative-type identification.
  • a site may be positively determined to be either guanine or cytosine for an individual homozygous at that site, or both guanine and cytosine, if the individual is heterozygous at that site.
  • the site may be negatively determined to be not guanine (and thus cytosine/cytosine) or not cytosine (and thus guanine/guanine).
  • a PS in the target region may also be assayed before or after amplification using one of several hybridization-based methods known in the art.
  • allele-specific oligonucleotides are utilized in performing such methods.
  • the allele-specific oligonucleotides may be used as differently labeled probe pairs, with one member of the pair showing a perfect match to one variant of a target sequence and the other member showing a perfect match to a different variant.
  • more than one PS may be detected at once using a set of allele-specific oligonucleotides or oligonucleotide pairs.
  • the members of the set have melting temperatures within 5° C., and more preferably within 2° C., of each other when hybridizing to each of the polymorphic sites being detected.
  • Hybridization of an allele-specific oligonucleotide to a target polynucleotide may be performed with both entities in solution, or such hybridization may be performed when either the oligonucleotide or the target polynucleotide is covalently or noncovalently affixed to a solid support. Attachment may be mediated, for example, by antibody-antigen interactions, poly-L-Lys, streptavidin or avidin-biotin, salt bridges, hydrophobic interactions, chemical linkages, UV cross-linking baking, etc. Allele-specific oligonucleotides may be synthesized directly on the solid support or attached to the solid support subsequent to synthesis.
  • Solid-supports suitable for use in detection methods of the invention include substrates made of silicon, glass, plastic, paper and the like, which may be formed, for example, into wells (as in 96-well plates), slides, sheets, membranes, fibers, chips, dishes, and beads.
  • the solid support may be treated, coated or derivatized to facilitate the immobilization of the allele-specific oligonucleotide or target nucleic acid.
  • Detecting the nucleotide or nucleotide pair at a PS of interest may also be determined using a mismatch detection technique, including but not limited to the RNase protection method using riboprobes (Winter et al., Proc. Natl. Acad. Sci. USA 82:7575 (1985); Meyers et al., Science 230:1242 (1985)) and proteins which recognize nucleotide mismatches, such as the E. coli mutS protein (Modrich, Ann. Rev. Genet. 25:229-53 (1991)).
  • riboprobes Winter et al., Proc. Natl. Acad. Sci. USA 82:7575 (1985); Meyers et al., Science 230:1242 (1985)
  • proteins which recognize nucleotide mismatches such as the E. coli mutS protein (Modrich, Ann. Rev. Genet. 25:229-53 (1991)).
  • variant alleles can be identified by single strand conformation polymorphism (SSCP) analysis (Orita et al., Genomics 5:874-9 (1989); Humphries et al., in M OLECULAR D IAGNOSIS OF G ENETIC D ISEASES , Elles, ed., pp. 321-340, 1996) or denaturing gradient gel electrophoresis (DGGE) (Wartell et al., Nucl. Acids Res. 18:2699-706 (1990); Sheffield et al., Proc. Natl. Acad. Sci. USA 86:232-6 (1989)).
  • SSCP single strand conformation polymorphism
  • DGGE denaturing gradient gel electrophoresis
  • a polymerase-mediated primer extension method may also be used to identify the polymorphism(s).
  • Several such methods have been described in the patent and scientific literature and include the “Genetic Bit Analysis” method (WO 92/15712) and the ligase/polymerase mediated genetic bit analysis (U.S. Pat. No. 5,679,524. Related methods are disclosed in WO 91/02087, WO 90/09455, WO 95/17676, and U.S. Pat. Nos. 5,302,509 and 5,945,283. Extended primers containing the complement of the polymorphism may be detected by mass spectrometry as described in U.S. Pat. No. 5,605,798.
  • Another primer extension method is allele-specific PCR (Rua ⁇ o et al., 1989, supra; Rua ⁇ o et al., 1991, supra; WO 93/22456; Turki et al., J. Clin. Invest. 95:1635-41 (1995)).
  • multiple PSs may be investigated by simultaneously amplifying multiple regions of the nucleic acid using sets of allele-specific primers as described in WO 89/10414.
  • the genotype or haplotype for the NTRK1 gene of an individual may also be determined by hybridization of a nucleic acid sample containing one or both copies of the gene, mRNA, cDNA or fragment(s) thereof, to nucleic acid arrays and subarrays such as described in WO 95/112995.
  • the arrays would contain a battery of allele-specific oligonucleotides representing each of the PSs to be included in the genotype or haplotype.
  • the invention also provides a kit for determining whether an individual has an age of onset marker I or an age of onset marker II.
  • the kit comprises a set of one or more oligonucleotides designed for identifying at least one of the alleles at each PS in a set of one or more PSs, wherein the set of one or more PSs comprises (a) PS1, PS5, PS9, and PS11; (b) PS1, PS5, PS10, and PS11; (c) PS5, PS9, and PS11; (d) PS5, PS8, PS9, and PS11; (e) PS5, PS8, PS10, and PS11; (f) PS5, PS9, PS11, and PS12; (g) PS5, PS10, and PS1; (h) PS5, PS10, PS11, and PS12; (i) PS5, PS9, PS10, and PS11; 0) PS4, PS5, PS9, and PS11; (k) PS4, PS5, PS10, and PS11; (1) PS1, PS9, and PS11; (m) PS
  • the kit comprises a set of one or more oligonucleotides designed for identifying at least one of the alleles at each PS in a set of one or more PSs, wherein the set of one or more PSs is any of (a) PS1, PS5, PS9, and PS11; (b) PS1, PS5, PS10, and PS11; (c) PS5, PS9, and PS11; (d) PS5, PS8, PS9, and PS11; (e) PS5, PS8, PS10, and PS11; (f) PS5, PS9, PS11, and PS12; (g) PS5, PS10, and PS11; (h) PS5, PS10, PS11, and PS12; (i) PS5, PS9, PS10, and PS11; (j) PS4, PS5, PS9, and PS11; (k) PS4, PS5, PS10, and PS11; (l) PS1, PS9, and PS11; (m) PS1, PS9, PS11, and PS12; (n) PS1, PS10, and PS11; (o) PS1,
  • the set of one or more oligonucleotides is designed for identifying both alleles at each PS in the set of one or more PSs.
  • the individual is Caucasian.
  • the kit further comprises a manual with instructions for (a) performing one or more reactions on a human nucleic acid sample to identify the allele or alleles present in the individual at each PS in the set of one or more PSs, and (b) determining if the individual has an age of onset marker I or an age of onset marker II based on the identified allele or alleles.
  • the linkage disequilibrium between the linked haplotype and at least one of haplotypes (1)-(112) in Table 1 has a delta squared value selected from the group consisting of at least 0.75, at least 0.80, at least 0.85, at least 0.90, at least 0.95, and 1.0.
  • the linkage disequilibrium between the allele at a substituting PS in the substitute haplotype and the allele at a substituted PS in any of haplotypes (1)-(112) in Table 1 has a delta squared value selected from the group consisting of at least 0.75, at least 0.80, at least 0.85, at least 0.90, at least 0.95, and 1.0.
  • an “oligonucleotide” is a probe or primer capable of hybridizing to a target region that contains, or that is located close to, a PS of interest.
  • the oligonucleotide has less than about 100 nucleotides. More preferably, the oligonucleotide is 10 to 35 nucleotides long. Even more preferably, the oligonucleotide is between 15 and 30, and most preferably, between 20 and 25 nucleotides in length. The exact length of the oligonucleotide will depend on the nature of the genomic region containing the PS as well as the genotyping assay to be performed and is readily determined by the skilled artisan.
  • oligonucleotides used to practice the invention may be comprised of any phosphorylation state of ribonucleotides, deoxyribonucleotides, and acyclic nucleotide derivatives, and other functionally equivalent derivatives.
  • oligonucleotides may have a phosphate-free backbone, which may be comprised of linkages such as carboxymethyl, acetamidate, carbamate, polyamide (peptide nucleic acid (PNA)) and the like (Varma, in M OLECULAR B IOLOGY AND B IOTECHNOLOGY , A C OMPREHENSIVE D ESK R EFERENCE , Meyers, ed., pp.
  • Oligonucleotides of the invention may be prepared by chemical synthesis using any suitable methodology known in the art, or may be derived from a biological sample, for example, by restriction digestion.
  • the oligonucleotides may be labeled, according to any technique known in the art, including use of radiolabels, fluorescent labels, enzymatic labels, proteins, haptens, antibodies, sequence tags and the like.
  • Oligonucleotides of the invention must be capable of specifically hybridizing to a target region of a polynucleotide containing a desired locus.
  • specific hybridization means the oligonucleotide forms an anti-parallel double-stranded structure with the target region under certain hybridizing conditions, while failing to form such a structure when incubated with another region in the polynucleotide or with a polynucleotide lacking the desired locus under the same hybridizing conditions.
  • the oligonucleotide specifically hybridizes to the target region under conventional high stringency conditions.
  • a nucleic acid molecule such as an oligonucleotide or polynucleotide is said to be a “perfect” or “complete” complement of another nucleic acid molecule if every nucleotide of one of the molecules is complementary to the nucleotide at the corresponding position of the other molecule.
  • a nucleic acid molecule is “substantially complementary” to another molecule if it hybridizes to that molecule with sufficient stability to remain in a duplex form under conventional low-stringency conditions.
  • an oligonucleotide primer may have a non-complementary fragment at its 5′ end, with the remainder of the primer being complementary to the target region.
  • non-complementary nucleotides may be interspersed into the probe or primer as long as the resulting probe or primer is still capable of specifically hybridizing to the target region.
  • oligonucleotides of the invention useful in determining if an individual has an age of onset marker I or an age of onset marker II, are allele-specific oligonucleotides.
  • ASO allele-specific oligonucleotide
  • allele-specificity will depend upon a variety of readily optimized stringency conditions, including salt and formamide concentrations, as well as temperatures for both the hybridization and washing steps.
  • Allele-specific oligonucleotides of the invention include ASO probes and ASO primers.
  • ASO probes which usually provide good discrimination between different alleles are those in which a central position of the oligonucleotide probe aligns with the polymorphic site in the target region (e.g., approximately the 7 th or 8 th position in a 15mer, the 8 th or 9 th position in a 16mer, and the 10 th or 112 th position in a 20mer).
  • An ASO primer of the invention has a 3′ terminal nucleotide, or preferably a 3′ penultimate nucleotide, that is complementary to only one of the nucleotide alleles of a particular SNP, thereby acting as a primer for polymerase-mediated extension only if that nucleotide allele is present at the PS in the sample being genotyped.
  • ASO probes and primers hybridizing to either the coding or noncoding strand are contemplated by the invention.
  • a preferred ASO probe for detecting the alleles at each of PS1, PS4, PS5, PS7, PS8, PS9, PS10, PS11, and PS12, is listed in Table 4. Additionally, detection of the alleles at each of PS1, PS4, PS5, PS7, PS8, PS9, PS10, PS11, and PS12 could be accomplished by utilization of the complement of these ASO probes.
  • a preferred ASO forward and reverse primer for detecting the alleles at each of PS1, PS4, PS5, PS7, PS8, PS9, PS10, PS11, and PS12 is listed in Table 4. TABLE 4 Preferred ASOs for Detecting Alleles at PSs in Haplotypes Comprising Preferred Embodiments of Age of Onset Markers I and II 1
  • ASO ASO
  • ASO Probe Forward Primer Reverse Primer SEQ SEQ SEQ ID ID ID PS Sequence NO. Sequence NO.
  • oligonucleotides useful in practicing the invention hybridize to a target region located one to several nucleotides downstream of a PS in an age of onset marker. Such oligonucleotides are useful in polymerase-mediated primer-extension methods for detecting an allele at one of the PSs in the markers described herein and therefore such oligonucleotides are referred to herein as “primer-extension oligonucleotides.”
  • the 3′-terminus of a primer-extension oligonucleotide is a deoxynucleotide complementary to the nucleotide located immediately adjacent to the PS.
  • a particularly preferred forward and reverse primer-extension oligonucleotide for detecting the alleles at each of PS1, PS4, PS5, PS7, PS8, PS9, PS10, PS11, and PS12 is listed in Table 5. Termination mixes are chosen to terminate extension of the oligonucleotide at the PS of interest, or one base thereafter, depending on the alternative nucleotides present at the PS. TABLE 5 Preferred Primer Extension Oligonucleotides for Detecting Alleles at PSs in Haplotypes Comprising Preferred Embodiments of Age of Onset Markers I and II Forward Reverse Primer Extension Primer Extension PS Sequence SEQ ID NO. Sequence SEQ ID NO.
  • the oligonucleotides in a kit of the invention have different labels to allow probing of the identity of nucleotides or nucleotide pairs at two or more PSs simultaneously.
  • the oligonucleotides in a kit of the invention may also be immobilized on or synthesized on a solid surface such as a microchip, bead, or glass slide (see, e.g., WO 98/20020 and WO 98/20019).
  • a solid surface such as a microchip, bead, or glass slide
  • Such immobilized oligonucleotides may be used in a variety of polymorphism detection assays, including but not limited to probe hybridization and polymerase extension assays.
  • Immobilized oligonucleotides useful in practicing the invention may comprise an ordered array of oligonucleotides designed to rapidly screen a nucleic acid sample for polymorphisms in multiple genes at the same time.
  • Kits of the invention may also contain other components such as hybridization buffer (e.g., where the oligonucleotides are to be used as allele-specific probes) or dideoxynucleotide triphosphates (ddNTPs; e.g., where the alleles at the polymorphic sites are to be detected by primer extension).
  • the set of oligonucleotides consists of primer-extension oligonucleotides.
  • the kit may also contain a polymerase and a reaction buffer optimized for primer-extension mediated by the polymerase.
  • kits may also include detection reagents, such as biotin- or fluorescent-tagged oligonucleotides or ddNTPs and/or an enzyme-labeled antibody and one or more substrates that generate a detectable signal when acted on by the enzyme.
  • detection reagents such as biotin- or fluorescent-tagged oligonucleotides or ddNTPs and/or an enzyme-labeled antibody and one or more substrates that generate a detectable signal when acted on by the enzyme.
  • each of the oligonucleotides and all other reagents in the kit have been quality tested for optimal performance in an assay for determining the alleles at a set of PSs comprising an age of onset marker I or age of onset marker II.
  • the invention provides a method for predicting the age of onset of AD in an individual at risk for developing AD.
  • the method comprises determining whether the individual has an age of onset marker I or an age of onset marker II, and making an age of onset prediction based on the results of the determining step.
  • the determination of the age of onset marker present in an individual can be made using one of the direct or indirect methods described herein.
  • the determining step comprises identifying for one or both copies of the genomic locus present in the individual the identity of the nucleotide or nucleotide pair at the set of PSs comprising the selected age of onset marker.
  • the determining step may comprise consulting a data repository that states the individual's copy number for the haplotypes comprising one of the age of onset markers I or age of onset markers II.
  • the data repository may be the individual's medical records or a medical data card. In preferred embodiments, the individual is Caucasian.
  • the prediction is that the individual's age of onset of AD will be between 71.6 and 73.3, and if the individual is determined to have an age of onset marker II, then the prediction is that the individual's age of onset of AD will be between 65.3 and 70.5.
  • the invention further provides a method for delaying the onset of AD in an individual at risk for developing AD.
  • the method comprises determining whether the individual has an age of onset marker I or an age of onset marker II, and making a treatment decision based upon the results of the determining step.
  • the determining step comprises identifying for one or both copies of the genomic locus present in the individual the identity of the nucleotide or nucleotide pair at the set of PSs comprising the selected haplotype.
  • the determining step may comprise consulting a data repository that states the individual's copy number for a haplotype comprising an age of onset marker I or an age of onset marker II.
  • the data repository may be the individual's medical records or a medical data card. In preferred embodiments, the individual is Caucasian.
  • the treatment decision is to prescribe to the individual a compound effective in delaying the onset of AD, wherein the compound is prescribed to the individual at an age below that of the lower confidence interval of the least square mean of age of onset for the age of onset marker I. If the individual is determined to have an age of onset marker II, the treatment decision is to prescribe to the individual at an age below that of the lower confidence interval of the least square mean of age of onset for the age of onset marker II.
  • the lower confidence interval of the least square mean of age of onset for an age of onset marker I ranges from 69.8 to 70.5
  • the lower confidence interval of the least square mean of age of onset for an age of onset marker II ranges from 65.3 to 65.9.
  • an article of manufacture comprises a pharmaceutical formulation and at least one indicium identifying a population for which the pharmaceutical formulation is indicated.
  • the pharmaceutical formulation comprises, as at least one active ingredient, a compound effective in delaying the onset of AD in an individual at risk for developing AD.
  • the pharmaceutical formulation may be regulated and the indicium may comprise the approved label for the pharmaceutical formulation.
  • the identified population is one that is at risk for developing AD, and is further partially or wholly defined by having an age of onset marker I or an age of onset marker II, wherein a trial population of individuals having an age of onset marker I exhibit a later age of onset of AD than a trial population of individuals having an age of onset marker II.
  • the identified population preferably may be further defined as Caucasian.
  • a population wholly defined by having an age of onset marker I or II is one for which there are no other factors which should be considered in identifying the population for which the pharmaceutical formulation is indicated.
  • a population that is partially defined by having an age of onset marker I or II is one for which other factors may be pertinent to identification of the population for which the pharmaceutical formulation is indicated. Examples of other such factors are age, weight, gender, disease state, possession of other genetic markers or biomarkers, or the like.
  • the pharmaceutical formulation may be formulated, in any way known in the art, for any mode of delivery (i.e., oral), and any mode of release (i.e., sustained release).
  • the pharmaceutical formulation is a tablet or capsule and the article may further comprise an additional indicium comprising the color or shape of the table or capsule.
  • the article may further comprise an additional indicium comprising a symbol stamped on the tablet or capsule, or a symbol or logo printed on the approved label.
  • the approved label may comprise a statement that the pharmaceutical formulation is indicated for delaying the onset of AD in an individual at risk for developing AD.
  • the approved label may further state the lower confidence interval of the least square mean of age of onset of AD for individuals having an age of onset marker I, and the lower confidence interval of the least square mean of age of onset of AD for individuals having an age of onset marker II.
  • An additional embodiment of the article of manufacture provided by the invention comprises packaging material and a pharmaceutical formulation contained within said packaging material.
  • the pharmaceutical formulation comprises, as at least one active ingredient, a compound effective in delaying the onset of AD in an individual at risk for developing AD.
  • the packaging material may comprise a label stating that the pharmaceutical formulation is indicated for a population at risk for developing AD and which is partially or wholly defined by having an age of onset marker I or an age of onset marker II, and preferably further stating that a trial population of individuals having an age of onset marker I exhibit a later age of onset of AD than a trial population of individuals having an age of onset marker II.
  • the indicated population preferably may be further defined as Caucasian.
  • a method of manufacturing a drug product comprising, as at least one active ingredient, a compound effective in delaying the onset of AD in an individual at risk for developing AD.
  • the method comprises combining in a package a pharmaceutical formulation comprising the compound and a label that states that the formulation is indicated for delaying the onset of AD in a population at risk for developing AD and which is partially or wholly defined by having an age of onset marker I or an age of onset marker II, wherein a trial population having an age of onset marker I exhibits a later age of onset of AD than a trial population having an age of onset marker II.
  • the indicated population may be identified on the pharmaceutical formulation, on the label or on the package by at least one indicium, such as a symbol or logo, color, or the like.
  • the indicated population preferably may be further defined as Caucasian.
  • Detecting the presence of an age of onset marker I or an age of onset marker II in an individual is also useful in a method for seeking regulatory approval for marketing a pharmaceutical formulation for delaying the onset of AD in a population at risk for developing AD, wherein the population is partially or wholly defined by having an age of onset marker I or an age of onset marker II.
  • the method comprises conducting at least one clinical trial which comprises administering the pharmaceutical formulation to first and second groups of individuals at risk for developing AD, and administering a placebo to third and fourth groups of individuals at risk for developing AD, wherein each individual in the first and third groups has an age of onset marker I, and each individual in the second and fourth groups has an age of onset marker II, demonstrating that the first group exhibits a later age of onset of AD than the third group, and demonstrating that the second group exhibits a later age of onset than the fourth group, and filing with a regulatory agency an application for marketing approval of the pharmaceutical formulation with a label stating that the pharmaceutical formulation is indicated for delaying the onset of AD in individuals at risk for developing AD.
  • the regulatory agency is the United States Food and Drug Administration (FDA) or the European Agency for the Evaluation of Medicinal Products (EMEA), or a future equivalent of these agencies.
  • the clinical trial may be conducted by recruiting individuals at risk for developing AD, determining whether they have an age of onset marker I or an age of onset marker II, and assigning them to the first and third groups if they have an age of onset marker I, and assigning them to the second and fourth groups if they have an age of onset marker II.
  • the individuals in each of the first and second groups are preferably administered the same dose of the pharmaceutical formulation, and the individuals in each of the third and fourth groups are preferably administered the same does of the placebo.
  • the regulatory agency may be any person or group authorized by the government of a country anywhere in the world to control the marketing or distribution of drugs in that country.
  • the regulatory agency is authorized by the government of a major industrialized country, such as Australia, Canada, China, a member of the European Union, Japan, and the like.
  • Most preferably the regulatory agency is authorized by the government of the United States and the type of application for approval that is filed will depend on the legal requirements set forth in the last enacted version of the Food, Drug and Cosmetic Act that are applicable for the pharmaceutical formulation and may also include other considerations such as the cost of making the regulatory filing and the marketing strategy for the composition.
  • the application might be a paper NDA, a supplemental NDA or an abbreviated NDA, but the application would be a full NDA if the pharmaceutical formulation has never been approved before; with these terms having the meanings applied to them by those skilled in the pharmaceutical arts or as defined in the Drug Price Competition and Patent Term Restoration Act of 1984.
  • a method for marketing a drug product comprising promoting to a target audience the use of a drug product for delaying the onset of AD in a population at risk for developing AD, wherein the population is partially or wholly defined by having an age of onset marker I or an age of onset marker II, wherein the drug product comprises a compound effective in delaying the onset of AD, and wherein a trial population of individuals having an age of onset marker I exhibit a later age of onset of AD than a trial population having an age of onset marker II.
  • the target audience can be members of a group that is in position to influence prescription or purchase of the drug product.
  • groups include physicians, pharmacists, insurance companies and health maintenance organizations, individuals at risk for developing AD, and government agencies such as those involved in providing or regulating medical insurance and those involved in regulating the marketing of drugs.
  • the promoting step can employ printed publications such as medical journals and consumer magazines, radio and television advertisements, and public presentations such as presentations at medical and scientific conferences.
  • the drug product is approved for marketing to delay the onset of AD in the population, and the promoting step includes a statement that relates the approved drug product to its appearance, e.g., the color or shape of a tablet or capsule formulation, or some design stamped or embossed thereon.
  • the individual's NTRK1 haplotype content or age of onset marker may be determined by consulting a data repository such as the individual's patient records, a medical data card, a file (e.g., a flat ASCII file) accessible by a computer or other electronic or non-electronic media on which information about the individual's NTRK1 haplotype content or age of onset marker can be stored.
  • a data repository such as the individual's patient records, a medical data card, a file (e.g., a flat ASCII file) accessible by a computer or other electronic or non-electronic media on which information about the individual's NTRK1 haplotype content or age of onset marker can be stored.
  • a medical data card is a portable storage device such as a magnetic data card, a smart card, which has an on-board processing unit and which is sold by vendors such as Siemens of Kunststoff Germany, or a flash-memory card.
  • the medical data card may be, but does not have to be, credit-card sized so that it easily fits into pocketbooks, wallets and other such objects carried by the individual.
  • the medical data card may be swiped through a device designed to access information stored on the data card.
  • portable data storage devices other than data cards can be used. For example, a touch-memory device, such as the “i-button” produced by Dallas Semiconductor of Dallas, Tex.
  • information about an individual's NTRK1 haplotype content or age of onset marker can be incorporated into objects such as jewelry.
  • the data storage device may be implemented so that it can wirelessly communicate with routing/intelligence devices through IEEE 802.112 wireless networking technology or through other methods well known to the skilled artisan.
  • information about an individual's haplotype content or age of onset marker can also be stored in a file accessible by a computer; such files may be located on various media, including: a server, a client, a hard disk, a CD, a DVD, a personal digital assistant such as a Palm Pilot, a tape, a zip disk, the computer's internal ROM (read-only-memory) or the internet or worldwide web.
  • Other media for the storage of files accessible by a computer will be obvious to one skilled in the art.
  • any or all analytical and mathematical operations involved in practicing the methods of the present invention may be implemented by a computer.
  • the computer may execute a program that assigns NTRK1 haplotype pairs and/or an age of onset marker I or an age of onset marker II to individuals based on genotype data inputted by a laboratory technician or treating physician.
  • the computer may output the predicted change in cognitive function in age of onset to a galantamine following input of the individual's NTRK1 haplotype content or age of onset marker, which was either determined by the computer program or input by the technician or physician.
  • Data on which age of onset markers were detected in an individual may be stored as part of a relational database (e.g., an instance of an Oracle database or a set of ASCII flat files) containing other clinical and/or haplotype data for the individual.
  • a relational database e.g., an instance of an Oracle database or a set of ASCII flat files
  • These data may be stored on the computer's hard drive or may, for example, be stored on a CD ROM or on one or more other storage devices accessible by the computer.
  • the data may be stored on one or more databases in communication with the computer via a network.
  • compositions of the invention may be utilized in combination with identifying genotype(s) and/or haplotype(s) for other genomic regions.
  • This example illustrates the clinical and biochemical characterization of selected individuals in a cohort of 449 Caucasian patients diagnosed with AD, each of whom had previously participated in a clinical trial of galantamine.
  • Genomic DNA samples were isolated from blood samples obtained from each member of the cohort and genotyped at each of PS1-PS12 (Table 2) using the MassARRAY technology licensed from Sequenom (San Diego, Calif.).
  • this genotyping technology involves performing a homogeneous MassEXTEND assay (hME), in which an initial polymerase chain reaction is followed by an allele-specific oligonucleotide extension reaction in the same tube or plate well, and then detecting the extended oligonucleotide by MALDI-TOF mass spectrometry.
  • hME homogeneous MassEXTEND assay
  • a genomic DNA sample was amplified in a 8.0 ⁇ L multiplexed PCR reaction consisting of 2.5 ng genomic DNA (0.3 ng/ ⁇ L), 0.85 ⁇ L 10 ⁇ reaction buffer, 0.32 units Taq Polymerase, up to five sets of 0.4 pmol each of forward PCR primer (5′ to 3′) and reverse PCR primer (3′ to 5′) and 1.6 nmol each of dATP, dCTP, dGTP and dTTP.
  • PCR thermocycling conditions were: initial denaturation of 95° C. for 15 minutes followed by 45 cycles of 94° C. for 20 seconds, 56° C. for 30 seconds and 72° C. for 1 minute followed by a final extension of 72° C. for 3 minutes. Following the final extension, unincorporated deoxynucleotides were degraded by adding 0.48 units of Shrimp Alkaline Phosphatase (SAP) to the PCR reactions and incubation for 20 minutes at 37° C. followed by 5 minutes at 85° C. to inactivate the SAP.
  • SAP Shrimp Alkaline Phosphatase
  • Template-dependent primer extension reactions were then performed on the multiplexed PCR products by adding a 2.0 ⁇ L volume of an hME cocktail consisting of 720 pmol each of three dideoxynucleotides and 720 pmol of one deoxynucleotide, 8.6 pmol of an extension primer, 0.2 ⁇ L of 5 ⁇ Thermosequenase Reaction Buffer, and NanoPure grade water.
  • the thermocycling conditions for the mass extension reaction were: initial denaturation for 2 minutes at 94° C. followed by 40 cycles of 94° C. for 5 seconds, 40° C. for 5 seconds and 72° C. for 5 seconds.
  • Extension primers used to genotype each of the twelve CHRNA2 polymorphic sites are shown in Table 7 below: TABLE 7 Extension Primers for Genotyping NTRK1 Polymorphic Sites PS1 CCAGCAGGCTGCCCGGC (SEQ ID NO:72) PS2 TGCTCCCTCTTATCCCCTGTGA (SEQ ID NO:73) PS3 CAAGCACTGAAAAGGCCTGGGGAA (SEQ ID NO:74) PS4 GGTTTTCATGGGAATCTGGAAA (SEQ ID NO:75) PS5 CTGGATACCGGGGTGGG (SEQ ID NO:76) PS6 GAGTGCTCGGCAGGACTTCCA (SEQ ID NO:77) PS7 TGCCTCTACTGTTCTCTCAAT (SEQ ID NO:78) PS8 TGGGAGAGGAGACTGGGG (SEQ ID NO:79) PS9 TCTCCTTTTCTTGTTCACAGATCC (SEQ ID NO:80) PS1O ATGCCAAGCTGCTGGCTG (SEQ ID NO:81) PS11 CC
  • extension products were desalted prior to analysis by mass spectrometry by mixing them with AG50X8 NH 4 OAc cation exchange resin.
  • the desalted multiplexed extension products were applied onto a SpectroCHIPTM using the SpectroPOINTTM 24 pin applicator tool as per manufacturer's instructions (Sequenom Industrial Genomics, Inc. San Diego, Calif.).
  • the SpectroChipTM was loaded into a Bruker Biflex IIITM linear time-of flight mass spectrometer equipped with a SCOUT 384 ion source and data was acquired using XACQ 4.0, MOCTL 2.1, AutoXecute 4.2 and XMASS/XTOF 5.0.1 software on an Ultra 5TM work station (Sun Microsystems, Palo Alto Calif.). Mass spectrometry data was subsequently analyzed on a PC running Windows NT 4.0 (Microsoft, Seattle Wash.) with SpectroTYPERTM genotype calling software (Sequenom Industrial Genomics, Inc. San Diego, Calif.).
  • This example illustrates the deduction of haplotypes from the CHRNA2 genotyping data generated in Example 1.
  • Haplotypes were estimated from the unphased genotypes using a computer-implemented algorithm for assigning haplotypes to unrelated individuals in a population sample, essentially as described in WO 01/80156 (Genaissance Pharmaceuticals, Inc., New Haven, Conn.). In this method, haplotypes are assigned directly from individuals who are homozygous at all sites or heterozygous at no more than one of the variable sites. This list of haplotypes is then used to deconvolute the unphased genotypes in the remaining (multiply heterozygous) individuals.
  • a quality control analysis was performed on the deduced haplotypes, which included analysis of the frequencies of the haplotypes and individual SNPs therein for compliance with principles of Hardy-Weinberg equilibrium.
  • This example illustrates analysis of the NTRK1 haplotypes in Table 1 for association with individuals' responses to galantamine.
  • the statistical analyses compared age of onset of AD in individuals with zero copies vs. at least one copy (within an individual's genome) of a particular allele, using a logistic regression analysis on two-degrees of freedom to associate age of onset of AD with a particular haplotype.
  • the following covariates were also included: gender, family history, and smoking.
  • NTRK1 haplotypes of at least one polymorphism were identified that show a correlation with an individual's age of onset of AD. These NTRK1 haplotypes are shown above in Table 1, and the unadjusted (“Raw”) and adjusted (“Perm.”) p-values for these 112 haplotypes are shown below in Table 8. TABLE 8 NTRK1 Haplotypes Having Association with Age of Onset of Alzheimer's Disease Lower Upper Confidence Confidence Least Square Interval of Interval of Mean of Least Square Least Square Subject Count Age of Mean of Age Mean of Age for Haplotype Onset (# of of Onset (# of of Onset (# of Haplotype Perm.
  • each of the 112 haplotypes shows a correlation with an individual's age of onset of AD.
  • the Least Square Mean of Age of Onset column indicates the average age of onset of AD in individuals, in this cohort, having zero copies or at least one copy of a particular haplotypelikelihood that an individual with at least one copy of a particular haplotype will respond to galantamine as compared to an individual with zero copies of that haplotype.

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US20050255495A1 (en) * 2003-12-15 2005-11-17 Genaissance Pharmaceuticals SLC5A7 genetic markers associated with age of onset of Alzheimer's disease
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